BIOL 200 Midterm Review Exam
Questions and Answers
Central Dogma - ANSWER-DNA > RNA > Protein
Nucleotides - ANSWER-base, sugar, phosphate
Glycosidic Bond - ANSWER-Base and sugar bond
Nucleotide monomers - ANSWER-phosphates = acidic characteristics, covalently
bonded to suger (phosphodiester bond)
Hydrogenous base = covalently bond to sugar
Sugar
Purines - ANSWER-2 ring base, Adenine, Guanine
Pyramidines - ANSWER-1 ring base, RNA = uracil, cytosine, DNA = thymine, cytosine
Nucleoside - ANSWER-base, sugar
Amino Acid - ANSWER-building blocks of polypeptides, determines the shape of the
polypeptide, 20 types
Protein functions - ANSWER-catlysis, transport, signalling, structure, motor, regulatory
(control protein activity/gene function)
Amino Acid Structure - ANSWER-Amino end (N-terminus), Carboxyl end (C-terminus),
R groups
Special a.a. - ANSWER-Cysteine, glycine, proline
Cysteine - ANSWER-special a.a with sulfhydryl group, form disulfide bonds
Glycine - ANSWER-special a.a. with H symmetrical, intra/inter cross linking
Proline - ANSWER-special a.a. rigid ring structure
DNA shape - ANSWER-5' end: free phosphate group attached to sugar phosphodiester
bond: links nucleotides
3' end: free hydroxyl group on terminal end sugar
,DNA "backbone" - ANSWER-repeating phosphate-pentose units, holds no info
outside of dbl bond
within DNA structure
3D structure of DNA - ANSWER-watson and crick, 2 polynucleotide strands wound
together to form dbl helix (anti //), bases stacked
Base pairing - ANSWER-complementary base
T dbl bonds to A, C triple bonds to G (stronger = more H bonds)
Right-handed Helix DNA - ANSWER-most DNA in cells
B DNA - ANSWER-major and minor groove, important for DNA-protein interactions, ex:
TBP
R-H helix
A DNA - ANSWER-low humidity or high [salt], B DNA turns into A DNA
RNA-DNA, RNA-RNA exist in this form
R-H helix
- smaller, wider
Z DNA - ANSWER-short DNA molecule of alternating purines and pyramidines
formed after transcription, tag for transcribed genes
L-H helix
- taller, longer
DNA denaturation and renaturation - ANSWER-important for DNA
replication/transcription
unzipping and re-annealing of DNA
RNA secondary structures - ANSWER-hairpin, stem-loop
RNA tertiary structure - ANSWER-pseudoknot
Primary structure of protein - ANSWER-a.a. sequence
amino end, amide groups, r groups, carboxyl ends
Peptide Bond - ANSWER-linkange of one a.a. to another, on C terminus linking to next
N terminus
Residue - ANSWER-amino acid
Secondary structure of protein - ANSWER-local folding
alpha-helix: stabilized by H bonds
beta sheet: 5-8 residues, r groups away/toward you, laterally packed beta strands, // or
anti //
, Beta turn: most common, 3-4 residues, glycine/proline twists and turns
Tertiary structure of protein - ANSWER-long range folding
stabilized by hydrophobic interactions b/w non-polar side chains
H bonds b/w polar side chains
Disulfide bonds b/w cysteine residues (covalent bond)
Quaternary structure of protein - ANSWER-multi-meric structure
pores (4 proteins) = potassium ion channel protein
Supramolecule structure of protein - ANSWER-large-scale assembly
10-100 polypeptides chains
general transcription factors: RNA polymerase, mediator complex, promotor, pre-
initiation transcription complex
Motifs - ANSWER-combos of secondary structure proteins
Coil-Coil Motif - ANSWER-hydrophobic interactions
fibrous proteins
ex: collagen
Helix-loop-helix Motif - ANSWER-ionic bonds involving Ca2+
ex: Ca2+ binding proteins
Zinc-finger Motif - ANSWER-contains Zn2+
ex: RNA, DNA, binding proteins
Domains - ANSWER-need these for certain proteins to function
ex: pyruvate kinase needs 3 domains
Reshuffling of motifs and domains - ANSWER-new proteins made
Ingredients for transcription in bacteria - ANSWER-DNA template, ribonucleotides
(monomers for RNA polymerization), RNA polymerase (catalyze synthesis of RNA
Ist step of transcription - ANSWER-Initiation
- polymerase binds to promoter (upstream of gene) in duplex DNA
forms "closed complex"
- polymerase melts duplex DNA
forms "open complex"
- polymerase catalyzes phosphodiester linkage of two initial rNTPs
rNTP - ANSWER-ribonucleotide tri-phosphate, building blocks of RNA synthesis
N = G, C, A, U
2nd step of transcription - ANSWER-Elongation
Questions and Answers
Central Dogma - ANSWER-DNA > RNA > Protein
Nucleotides - ANSWER-base, sugar, phosphate
Glycosidic Bond - ANSWER-Base and sugar bond
Nucleotide monomers - ANSWER-phosphates = acidic characteristics, covalently
bonded to suger (phosphodiester bond)
Hydrogenous base = covalently bond to sugar
Sugar
Purines - ANSWER-2 ring base, Adenine, Guanine
Pyramidines - ANSWER-1 ring base, RNA = uracil, cytosine, DNA = thymine, cytosine
Nucleoside - ANSWER-base, sugar
Amino Acid - ANSWER-building blocks of polypeptides, determines the shape of the
polypeptide, 20 types
Protein functions - ANSWER-catlysis, transport, signalling, structure, motor, regulatory
(control protein activity/gene function)
Amino Acid Structure - ANSWER-Amino end (N-terminus), Carboxyl end (C-terminus),
R groups
Special a.a. - ANSWER-Cysteine, glycine, proline
Cysteine - ANSWER-special a.a with sulfhydryl group, form disulfide bonds
Glycine - ANSWER-special a.a. with H symmetrical, intra/inter cross linking
Proline - ANSWER-special a.a. rigid ring structure
DNA shape - ANSWER-5' end: free phosphate group attached to sugar phosphodiester
bond: links nucleotides
3' end: free hydroxyl group on terminal end sugar
,DNA "backbone" - ANSWER-repeating phosphate-pentose units, holds no info
outside of dbl bond
within DNA structure
3D structure of DNA - ANSWER-watson and crick, 2 polynucleotide strands wound
together to form dbl helix (anti //), bases stacked
Base pairing - ANSWER-complementary base
T dbl bonds to A, C triple bonds to G (stronger = more H bonds)
Right-handed Helix DNA - ANSWER-most DNA in cells
B DNA - ANSWER-major and minor groove, important for DNA-protein interactions, ex:
TBP
R-H helix
A DNA - ANSWER-low humidity or high [salt], B DNA turns into A DNA
RNA-DNA, RNA-RNA exist in this form
R-H helix
- smaller, wider
Z DNA - ANSWER-short DNA molecule of alternating purines and pyramidines
formed after transcription, tag for transcribed genes
L-H helix
- taller, longer
DNA denaturation and renaturation - ANSWER-important for DNA
replication/transcription
unzipping and re-annealing of DNA
RNA secondary structures - ANSWER-hairpin, stem-loop
RNA tertiary structure - ANSWER-pseudoknot
Primary structure of protein - ANSWER-a.a. sequence
amino end, amide groups, r groups, carboxyl ends
Peptide Bond - ANSWER-linkange of one a.a. to another, on C terminus linking to next
N terminus
Residue - ANSWER-amino acid
Secondary structure of protein - ANSWER-local folding
alpha-helix: stabilized by H bonds
beta sheet: 5-8 residues, r groups away/toward you, laterally packed beta strands, // or
anti //
, Beta turn: most common, 3-4 residues, glycine/proline twists and turns
Tertiary structure of protein - ANSWER-long range folding
stabilized by hydrophobic interactions b/w non-polar side chains
H bonds b/w polar side chains
Disulfide bonds b/w cysteine residues (covalent bond)
Quaternary structure of protein - ANSWER-multi-meric structure
pores (4 proteins) = potassium ion channel protein
Supramolecule structure of protein - ANSWER-large-scale assembly
10-100 polypeptides chains
general transcription factors: RNA polymerase, mediator complex, promotor, pre-
initiation transcription complex
Motifs - ANSWER-combos of secondary structure proteins
Coil-Coil Motif - ANSWER-hydrophobic interactions
fibrous proteins
ex: collagen
Helix-loop-helix Motif - ANSWER-ionic bonds involving Ca2+
ex: Ca2+ binding proteins
Zinc-finger Motif - ANSWER-contains Zn2+
ex: RNA, DNA, binding proteins
Domains - ANSWER-need these for certain proteins to function
ex: pyruvate kinase needs 3 domains
Reshuffling of motifs and domains - ANSWER-new proteins made
Ingredients for transcription in bacteria - ANSWER-DNA template, ribonucleotides
(monomers for RNA polymerization), RNA polymerase (catalyze synthesis of RNA
Ist step of transcription - ANSWER-Initiation
- polymerase binds to promoter (upstream of gene) in duplex DNA
forms "closed complex"
- polymerase melts duplex DNA
forms "open complex"
- polymerase catalyzes phosphodiester linkage of two initial rNTPs
rNTP - ANSWER-ribonucleotide tri-phosphate, building blocks of RNA synthesis
N = G, C, A, U
2nd step of transcription - ANSWER-Elongation
